RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6963
(212 letters)
>gnl|CDD|238083 cd00143, PP2Cc, Serine/threonine phosphatases, family 2C, catalytic
domain; The protein architecture and deduced catalytic
mechanism of PP2C phosphatases are similar to the PP1,
PP2A, PP2B family of protein Ser/Thr phosphatases, with
which PP2C shares no sequence similarity.
Length = 254
Score = 113 bits (284), Expect = 7e-31
Identities = 43/119 (36%), Positives = 61/119 (51%), Gaps = 7/119 (5%)
Query: 97 YKVGASCMQGWRITMEDAHSHILSLPDDPGTAFFAVYDGHGGSKIAQFAGKHLHKYIVK- 155
+ G S G R T EDA +L ++ F V+DGHGG +FA K L + +++
Sbjct: 1 FSAGVSDKGGDRKTNEDAVVIKPNL-NNEDGGLFGVFDGHGGHAAGEFASKLLVEELLEE 59
Query: 156 ---TREFKEGNITEALKKGFMDLDAAMLD--DDALKDELAGTTAICILIKDNILYCRNV 209
T E +I EAL+K F+ D +L+ D D +GTTA+ LI+ N LY NV
Sbjct: 60 LEETLTLSEEDIEEALRKAFLRADEEILEEAQDEPDDARSGTTAVVALIRGNKLYVANV 118
>gnl|CDD|214625 smart00332, PP2Cc, Serine/threonine phosphatases, family 2C,
catalytic domain. The protein architecture and deduced
catalytic mechanism of PP2C phosphatases are similar to
the PP1, PP2A, PP2B family of protein Ser/Thr
phosphatases, with which PP2C shares no sequence
similarity.
Length = 252
Score = 110 bits (278), Expect = 5e-30
Identities = 45/120 (37%), Positives = 67/120 (55%), Gaps = 8/120 (6%)
Query: 93 QNPLYKVGASCMQGWRITMEDAHSHILSLPDDPGTAFFAVYDGHGGSKIAQFAGKHLHKY 152
+N + G S MQG R MEDAH L D FF V+DGHGGS+ A+F K+L +
Sbjct: 5 KNLGLRYGLSSMQGVRKPMEDAHVITPDLSDS--GGFFGVFDGHGGSEAAKFLSKNLPEI 62
Query: 153 IVKTREFKEG---NITEALKKGFMDLDAAMLDDDALKDELAGTTAICILIKDNILYCRNV 209
+ + ++ ++ EAL+K F+ D +L++ + L+G+TA+ LI N LY NV
Sbjct: 63 LAEELIKEKDELEDVEEALRKAFLSTDEEILEE---LEALSGSTAVVALISGNKLYVANV 119
>gnl|CDD|215938 pfam00481, PP2C, Protein phosphatase 2C. Protein phosphatase 2C is
a Mn++ or Mg++ dependent protein serine/threonine
phosphatase.
Length = 252
Score = 100 bits (252), Expect = 4e-26
Identities = 48/117 (41%), Positives = 65/117 (55%), Gaps = 4/117 (3%)
Query: 97 YKVGASCMQGWRITMEDAHSHILSLPDDPG---TAFFAVYDGHGGSKIAQFAGKHLHKYI 153
VG MQG+R MEDAH +L G FFAV+DGHGGS+ A++AGKHL +
Sbjct: 1 LDVGGPRMQGFRKFMEDAHIAGKNLNASSGKDSFGFFAVFDGHGGSQAAKYAGKHLETIL 60
Query: 154 VKTREFKEGNITEALKKGFMDLDAAMLDDDALK-DELAGTTAICILIKDNILYCRNV 209
R F + +AL+K F++ D + D A D +G+TA+ LI+ LY NV
Sbjct: 61 ALRRSFLTLDKLDALRKSFLEADEELRSDAANHEDLSSGSTAVVALIRGQKLYVANV 117
>gnl|CDD|223704 COG0631, PTC1, Serine/threonine protein phosphatase [Signal
transduction mechanisms].
Length = 262
Score = 78.9 bits (195), Expect = 7e-18
Identities = 35/119 (29%), Positives = 53/119 (44%), Gaps = 12/119 (10%)
Query: 100 GASCMQGWRITMEDAHSHILSLPDDPGTAFFAVYDGHGGSKIAQFAGKHLHKYIVKTREF 159
G S + R EDA I + FAV DG GG + A K + + R F
Sbjct: 12 GLSDVGTVRKHNEDAFL-IKPNENGNLLLLFAVADGMGGHAAGEVASKLAVEALA--RLF 68
Query: 160 KEGN-------ITEALKKGFMDLDAAMLDDDALKDELA--GTTAICILIKDNILYCRNV 209
E N + E LK+ + + A+ ++ L +++ GTT + +LI+ N LY NV
Sbjct: 69 DETNFNSLNESLEELLKEAILKANEAIAEEGQLNEDVRGMGTTLVLLLIRGNKLYVANV 127
>gnl|CDD|215603 PLN03145, PLN03145, Protein phosphatase 2c; Provisional.
Length = 365
Score = 64.9 bits (158), Expect = 2e-12
Identities = 43/144 (29%), Positives = 65/144 (45%), Gaps = 15/144 (10%)
Query: 68 HPSGFSFAMGQTLTEP---VTNKDSSSVQNPLYKVGASCMQGWRITMEDAHSHILSLPDD 124
H S E N D+ + P+ + GA G R +MED + + + D
Sbjct: 35 HSSLVKTPASDISVENELTFENMDTEFI--PVVRSGAWADIGSRSSMEDVYICVDNFMSD 92
Query: 125 PG--------TAFFAVYDGHGGSKIAQFAGKHLHKYIVKTREFKEGNITEALKKGFMDLD 176
G +AF+ V+DGHGG A FA HL ++IV+ +F I + + F+ D
Sbjct: 93 FGLKNSEDGPSAFYGVFDGHGGKHAADFACYHLPRFIVEDEDFPR-EIEKVVSSAFLQTD 151
Query: 177 AAMLDDDALKDELA-GTTAICILI 199
A + +L LA GTTA+ L+
Sbjct: 152 TAFAEACSLDASLASGTTALAALV 175
>gnl|CDD|240318 PTZ00224, PTZ00224, protein phosphatase 2C; Provisional.
Length = 381
Score = 64.8 bits (158), Expect = 2e-12
Identities = 36/135 (26%), Positives = 65/135 (48%), Gaps = 12/135 (8%)
Query: 76 MGQTLTEPVTNKDSSSVQNPLYKVGASCMQGWRITMEDAHSHILSLPDDPGTAFFAVYDG 135
MG L +PV +K N +++ ++C+ G+R +MEDAH L FF V+DG
Sbjct: 1 MGIMLPKPVLSKLVDRAGNSIFRCASACVNGYRESMEDAHLLYL----TDDWGFFGVFDG 56
Query: 136 HGGSKIAQFAGKHLHKYIVKTREFKEGNIT-EALKKGFMDLDAAMLDDDALKDELAGTTA 194
H + +Q+ + + + K + +T E +++ +++D +D E T
Sbjct: 57 HVNDECSQYLARAWPQALEK----EPEPMTDERMEELCLEIDEEWMD---SGREGGSTGT 109
Query: 195 ICILIKDNILYCRNV 209
C+++KD L NV
Sbjct: 110 FCVIMKDVHLQVGNV 124
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 33.8 bits (77), Expect = 0.056
Identities = 14/32 (43%), Positives = 22/32 (68%)
Query: 35 EGEEKKYGGGRQEEEKKEEEEEDKEKCSGEED 66
+G GG +EEE++EEEEE++E+ EE+
Sbjct: 853 DGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEE 884
Score = 30.3 bits (68), Expect = 0.83
Identities = 14/34 (41%), Positives = 23/34 (67%)
Query: 32 DNNEGEEKKYGGGRQEEEKKEEEEEDKEKCSGEE 65
D + EE++ +EEE++EEEEE++E+ EE
Sbjct: 859 DGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEE 892
Score = 30.0 bits (67), Expect = 1.0
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 12/55 (21%)
Query: 27 AEHFPDNNEGEEKKYGGG------------RQEEEKKEEEEEDKEKCSGEEDSHP 69
AE+ + + E+ GGG +EEE++EEEEE++E+ EE+ P
Sbjct: 839 AENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEEP 893
Score = 28.0 bits (62), Expect = 4.9
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 32 DNNEGEEKKYGGGRQEEEKKEEEEEDKEKCSGE 64
+ E EE++ +EEE++EEEEE++E S E
Sbjct: 865 EEEEEEEEEEEEEEEEEEEEEEEEENEEPLSLE 897
>gnl|CDD|115046 pfam06364, DUF1068, Protein of unknown function (DUF1068). This
family consists of several hypothetical plant proteins
from Arabidopsis thaliana and Oryza sativa. The function
of this family is unknown.
Length = 176
Score = 30.0 bits (67), Expect = 0.53
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 14 LLRLPLG---SSLPNTAEHFPDNNEGEEKKYGGGRQEEEKKEEEE 55
LL +P +S + A+ P+ NE EK Y EE K+ E E
Sbjct: 56 LLTIPKELSNASFEDCAKQDPEVNEDTEKNYAELLTEELKQREAE 100
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 30.7 bits (69), Expect = 0.56
Identities = 23/114 (20%), Positives = 40/114 (35%), Gaps = 3/114 (2%)
Query: 18 PLGSSLPNTAEHFPDNNEGEEKKYGGGRQEEEKKEEEEEDKEKCSGEEDSHPSGFSFAMG 77
SS + EE+ +EEE++EEEE++ E+ GE++ G
Sbjct: 422 SKASSTSGESPSMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNG 481
Query: 78 QTLTEPVTNKDSSSVQNP--LYKVGASCMQGWRITMEDAHSHILSL-PDDPGTA 128
+++ + P + S M G E S+ P+ P
Sbjct: 482 SEEEMEGSSEGDGDGEEPEEDAERRNSEMAGISRMSEGQQPRGSSVQPESPQEE 535
>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family.
This family contains a number of defence peptides
secreted from the skin of amphibians, including the
opiate-like dermorphins and deltorphins, and the
antimicrobial dermoseptins and temporins. The alignment
for this family includes the signal peptide.
Length = 46
Score = 27.7 bits (62), Expect = 0.62
Identities = 12/21 (57%), Positives = 18/21 (85%)
Query: 47 EEEKKEEEEEDKEKCSGEEDS 67
EEEK+E+EEE++++ GEE S
Sbjct: 22 EEEKREDEEENEDEEEGEEQS 42
>gnl|CDD|192849 pfam11840, DUF3360, Protein of unknown function (DUF3360). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 489 to 517 amino acids in
length.
Length = 491
Score = 30.1 bits (68), Expect = 1.0
Identities = 31/117 (26%), Positives = 42/117 (35%), Gaps = 42/117 (35%)
Query: 73 SFAMGQTL---TEP-VTNKDSSSVQNPLYKVGASCMQGWRITMEDAHSHILSLPDDPGTA 128
+FAMG TEP + N NP+Y G GW++ + I LP A
Sbjct: 242 AFAMGAPFEFTTEPGLPN------LNPMYWWGEE--TGWQLGLPTLEHFIAVLP----FA 289
Query: 129 FFAV------YDGHGGSKIAQFAGKHLHKYIVKTREFKEGNITEALKKGFMDLDAAM 179
AV + GH R F+E N + +K MD+D M
Sbjct: 290 ILAVAMWSPDFLGH--------------------RVFQELNYPKKAEKVLMDVDDTM 326
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 29.4 bits (67), Expect = 1.2
Identities = 12/20 (60%), Positives = 17/20 (85%)
Query: 46 QEEEKKEEEEEDKEKCSGEE 65
EEE++EEEEE++E+ S EE
Sbjct: 301 AEEEEEEEEEEEEEEPSEEE 320
Score = 27.9 bits (63), Expect = 4.6
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 46 QEEEKKEEEEEDKEKCSGEED 66
EE++EEEEE++E+ EE+
Sbjct: 300 AAEEEEEEEEEEEEEEPSEEE 320
>gnl|CDD|227496 COG5167, VID27, Protein involved in vacuole import and degradation
[Intracellular trafficking and secretion].
Length = 776
Score = 29.6 bits (66), Expect = 1.4
Identities = 9/39 (23%), Positives = 16/39 (41%)
Query: 29 HFPDNNEGEEKKYGGGRQEEEKKEEEEEDKEKCSGEEDS 67
P + ++ Y + E + EE E +E+ ED
Sbjct: 357 SVPLEKQFDDILYFEKMEIENRNPEESEHEEEVEDYEDE 395
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 28.0 bits (63), Expect = 1.5
Identities = 11/21 (52%), Positives = 18/21 (85%)
Query: 47 EEEKKEEEEEDKEKCSGEEDS 67
EE+K+EEEEE++++ S EE +
Sbjct: 78 EEKKEEEEEEEEKEESEEEAA 98
Score = 27.6 bits (62), Expect = 2.2
Identities = 13/20 (65%), Positives = 16/20 (80%)
Query: 47 EEEKKEEEEEDKEKCSGEED 66
EEKKEEEEE++EK EE+
Sbjct: 77 AEEKKEEEEEEEEKEESEEE 96
Score = 26.1 bits (58), Expect = 7.8
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 6/30 (20%)
Query: 35 EGEEKKYGGGRQEEEKKEEEEEDKEKCSGE 64
EEKK EEE++EEE+E+ E+ +
Sbjct: 76 AAEEKK------EEEEEEEEKEESEEEAAA 99
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 27.7 bits (62), Expect = 2.0
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 42 GGGRQEEEKKEEEEEDKEKCSGEEDS 67
EEE++EEEEE++E+ EE++
Sbjct: 71 AAAAAEEEEEEEEEEEEEEEESEEEA 96
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein. This
family includes the radial spoke head proteins RSP4 and
RSP6 from Chlamydomonas reinhardtii, and several
eukaryotic homologues, including mammalian RSHL1, the
protein product of a familial ciliary dyskinesia
candidate gene.
Length = 481
Score = 28.5 bits (64), Expect = 2.9
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 28 EHFPDNNEGEEKKYGGGRQEEEKKEEEEEDKEK 60
+ EE++ +EEE++E EE + E+
Sbjct: 340 TWVNPEQKDEEEEQEDEEEEEEEEEPEEPEPEE 372
Score = 27.3 bits (61), Expect = 6.6
Identities = 9/36 (25%), Positives = 21/36 (58%)
Query: 34 NEGEEKKYGGGRQEEEKKEEEEEDKEKCSGEEDSHP 69
+G +++EE+++E+EE++E+ E+ P
Sbjct: 335 PQGRCTWVNPEQKDEEEEQEDEEEEEEEEEPEEPEP 370
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 28.6 bits (64), Expect = 3.3
Identities = 13/43 (30%), Positives = 18/43 (41%)
Query: 29 HFPDNNEGEEKKYGGGRQEEEKKEEEEEDKEKCSGEEDSHPSG 71
HF ++ K GR K EEE+ E+ EE+ G
Sbjct: 111 HFAKGDQSASAKKAKGRGRHASKLTEEEEDEEYLKEEEDGLGG 153
>gnl|CDD|147490 pfam05334, DUF719, Protein of unknown function (DUF719). This
family consists of several eukaryotic proteins of
unknown function.
Length = 180
Score = 27.9 bits (62), Expect = 3.3
Identities = 11/47 (23%), Positives = 16/47 (34%)
Query: 44 GRQEEEKKEEEEEDKEKCSGEEDSHPSGFSFAMGQTLTEPVTNKDSS 90
QE+ +K +E + S +F M LT V N
Sbjct: 53 VAQEKAEKGATGYSREDVDPNQGSQAVAGAFGMLSQLTSVVQNTGKK 99
>gnl|CDD|148511 pfam06936, Selenoprotein_S, Selenoprotein S (SelS). This family
consists of several mammalian selenoprotein S (SelS)
sequences. SelS is a plasma membrane protein and is
present in a variety of tissues and cell types. The
function of this family is unknown.
Length = 190
Score = 27.5 bits (61), Expect = 3.6
Identities = 13/44 (29%), Positives = 22/44 (50%)
Query: 48 EEKKEEEEEDKEKCSGEEDSHPSGFSFAMGQTLTEPVTNKDSSS 91
E++K+ EEE + + D G S+ + L + T + SSS
Sbjct: 105 EKQKQLEEEKRRQKIEMWDRMQEGKSYKVSAKLAQEATEETSSS 148
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 27.8 bits (62), Expect = 4.4
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 34 NEGEEKKYGGGRQEEEKKEEEEEDKEKCSGEED 66
+ +E+K E+++KE+ +EDKEK +E
Sbjct: 400 AKAKEEKLKQEENEKKQKEQADEDKEKRQKDER 432
>gnl|CDD|99859 cd06106, ScCit3_like, Saccharomyces cerevisiae (Sc) 2-methylcitrate
synthase Cit3-like. 2-methylcitrate synthase (2MCS)
catalyzes the condensation of propionyl-coenzyme A
(PrCoA) and oxaloacetate (OAA) to form 2-methylcitrate
and CoA. Citrate synthase (CS) catalyzes the
condensation of acetyl coenzyme A (AcCoA) with OAA to
form citrate and CoA, the first step in the citric acid
cycle (TCA or Krebs cycle). The overall CS reaction is
thought to proceed through three partial reactions and
involves both closed and open conformational forms of
the enzyme: a) the carbanion or equivalent is generated
from AcCoA by base abstraction of a proton, b) the
nucleophilic attack of this carbanion on OAA to generate
citryl-CoA, and c) the hydrolysis of citryl-CoA to
produce citrate and CoA. There are two types of CSs:
type I CS and type II CSs. Type I CSs are found in
eukarya, gram-positive bacteria, archaea, and in some
gram-negative bacteria and are homodimers with both
subunits participating in the active site. Type II CSs
are unique to gram-negative bacteria and are
homohexamers of identical subunits (approximated as a
trimer of dimers). ScCit3 is mitochondrial and functions
in the metabolism of PrCoA; it is a dual specificity CS
and 2MCS, having similar catalytic efficiency with both
AcCoA and PrCoA. The pattern of expression of the ScCIT3
gene follows that of the major mitochondrial CS gene
(CIT1, not included in this group) and its expression is
increased in the presence of a CIT1 deletion. This group
also contains Aspergillus nidulans 2MCS; a deletion of
the gene encoding this protein results in a strain
unable to grow on propionate. This group contains
proteins which functions exclusively as either a CS or a
2MCS, as well as those with relaxed specificity which
have dual functions as both a CS and a 2MCS.
Length = 428
Score = 27.9 bits (62), Expect = 4.5
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 86 NKDSSSVQNPLYKVGASCMQGWRITMEDAHSHILSLPDDPGTAFFAVY-DGHGGSKI 141
N DS Y+ G + W T+ED+ + I LP + VY +GHG KI
Sbjct: 144 NHDSKFAAA--YEKGIKKTEYWEPTLEDSLNLIARLPALAARIYRNVYGEGHGLGKI 198
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is functionally
equivalent to L7/L12 in bacteria and the P1 and P2
proteins in eukaryotes. L12p is homologous to P1 and P2
but is not homologous to bacterial L7/L12. It is located
in the L12 stalk, with proteins L10, L11, and 23S rRNA.
L12p is the only protein in the ribosome to occur as
multimers, always appearing as sets of dimers. Recent
data indicate that most archaeal species contain six
copies of L12p (three homodimers), while eukaryotes have
four copies (two heterodimers), and bacteria may have
four or six copies (two or three homodimers), depending
on the species. The organization of proteins within the
stalk has been characterized primarily in bacteria,
where L7/L12 forms either two or three homodimers and
each homodimer binds to the extended C-terminal helix of
L10. L7/L12 is attached to the ribosome through L10 and
is the only ribosomal protein that does not directly
interact with rRNA. Archaeal L12p is believed to
function in a similar fashion. However, hybrid ribosomes
containing the large subunit from E. coli with an
archaeal stalk are able to bind archaeal and eukaryotic
elongation factors but not bacterial elongation factors.
In several mesophilic and thermophilic archaeal species,
the binding of 23S rRNA to protein L11 and to the
L10/L12p pentameric complex was found to be
temperature-dependent and cooperative.
Length = 106
Score = 26.7 bits (59), Expect = 4.7
Identities = 9/28 (32%), Positives = 19/28 (67%)
Query: 37 EEKKYGGGRQEEEKKEEEEEDKEKCSGE 64
++ ++EE+KKEEE+E++E+ +
Sbjct: 73 AAEEKAEEKEEEKKKEEEKEEEEEEALA 100
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 27.9 bits (62), Expect = 4.8
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 4/35 (11%)
Query: 31 PDNNEGEEKKYGGGRQEEEKKEEEEEDKEKCSGEE 65
PDNNE E GR+E E +E EED+ + + E
Sbjct: 241 PDNNEDSE----AGREESEGSDESEEDEAEATDGE 271
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 27.6 bits (62), Expect = 5.4
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 45 RQEEEKKEEEEEDKEKCSGEE 65
++EE+KKEE E K S EE
Sbjct: 287 KKEEKKKEEREAKLAKLSPEE 307
>gnl|CDD|163497 TIGR03785, marine_sort_HK, proteobacterial dedicated sortase system
histidine kinase. This histidine kinase protein is
paired with an adjacent response regulator (TIGR03787)
gene. It co-occurs with a variant sortase enzyme
(TIGR03784), usually in the same gene neighborhood, in
proteobacterial species most of which are marine, and
with an LPXTG motif-containing sortase target conserved
protein (TIGR03788). Sortases and LPXTG proteins are far
more common in Gram-positive bacteria, where sortase
systems mediate attachment to the cell wall or
cross-linking of pilin structures. We give this
predicted sensor histidine kinase the gene symbol psdS,
for Proteobacterial Dedicated Sortase system Sensor
histidine kinase.
Length = 703
Score = 27.4 bits (61), Expect = 6.8
Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 13/66 (19%)
Query: 95 PLYKVGASCMQGWRITMEDAHSHILSLPDDPGTAFFAVYDGHG-GSKIAQFAGKHLHKYI 153
L +V + CMQG+++T L++P+ P G IAQ L K +
Sbjct: 559 DLSEVLSGCMQGYQMTYPP-QRFELNIPETPLVM-------RGSPELIAQM----LDKLV 606
Query: 154 VKTREF 159
REF
Sbjct: 607 DNAREF 612
>gnl|CDD|233708 TIGR02072, BioC, biotin biosynthesis protein BioC. This enzyme,
which is found in biotin biosynthetic gene clusters in
proteobacteria, firmicutes, green-sulfur bacteria,
fusobacterium and bacteroides, is believed to carry out
an enzymatic step prior to the formation of pimeloyl-CoA
(although attribution of this annotation is not
traceable). The enzyme appears related to
methyltransferases by homology [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 240
Score = 26.9 bits (60), Expect = 6.9
Identities = 18/68 (26%), Positives = 24/68 (35%), Gaps = 19/68 (27%)
Query: 130 FAVYDGHGGSKIAQFAGKHLHKYIVKTREFKE----------GNITEALKKGF------- 172
YD H +KI + K L + + F G +T AL K F
Sbjct: 6 AKTYDRH--AKIQREMAKRLLALLKEKGIFIPASVLDIGCGTGYLTRALLKRFPQAEFIA 63
Query: 173 MDLDAAML 180
D+ A ML
Sbjct: 64 NDISAGML 71
>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation
domain. The centromere protein B (CENP-B) dimerisation
domain is composed of two alpha-helices, which are
folded into an antiparallel configuration. Dimerisation
of CENP-B is mediated by this domain, in which monomers
dimerise to form a symmetrical, antiparallel,
four-helix bundle structure with a large hydrophobic
patch in which 23 residues of one monomer form van der
Waals contacts with the other monomer. This CENP-B
dimer configuration may be suitable for capturing two
distant CENP-B boxes during centromeric heterochromatin
formation.
Length = 101
Score = 26.3 bits (57), Expect = 7.0
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 35 EGEEKKYGGGRQEEEKKEEEEEDKEKCSGEED 66
EGEE +EE+ +E+EED ++ E+D
Sbjct: 7 EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDD 38
>gnl|CDD|218994 pfam06333, Med13_C, Mediator complex subunit 13 C-terminal.
Mediator is a large complex of up to 33 proteins that is
conserved from plants through fungi to humans - the
number and representation of individual subunits varying
with species. It is arranged into four different
sections, a core, a head, a tail and a kinase-activity
part, and the number of subunits within each of these is
what varies with species. Overall, Mediator regulates
the transcriptional activity of RNA polymerase II but it
would appear that each of the four different sections
has a slightly different function. Med13 is part of the
ancillary kinase module, together with Med12, CDK8 and
CycC, which in yeast is implicated in transcriptional
repression, though most of this activity is likely
attributable to the CDK8 kinase. The large Med12 and
Med13 proteins are required for specific developmental
processes in Drosophila, zebrafish, and Caenorhabditis
elegans but their biochemical functions are not
understood.
Length = 406
Score = 26.9 bits (60), Expect = 8.7
Identities = 7/40 (17%), Positives = 14/40 (35%)
Query: 56 EDKEKCSGEEDSHPSGFSFAMGQTLTEPVTNKDSSSVQNP 95
+ K + + P FS + P + + S +P
Sbjct: 226 DTDPKLVPDPPTQPIPFSRFNTSNSSTPQSTPCTLSFPSP 265
>gnl|CDD|221581 pfam12446, DUF3682, Protein of unknown function (DUF3682). This
domain family is found in eukaryotes, and is typically
between 125 and 136 amino acids in length.
Length = 133
Score = 26.3 bits (58), Expect = 8.7
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 43 GGRQEEEKKEEEEEDKEKCSGEE 65
G ++EE++EEEE +K++ S E
Sbjct: 92 GHTRQEEEEEEEENEKQQQSDEA 114
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.314 0.134 0.398
Gapped
Lambda K H
0.267 0.0697 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,063,988
Number of extensions: 1033020
Number of successful extensions: 1876
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1688
Number of HSP's successfully gapped: 87
Length of query: 212
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 119
Effective length of database: 6,812,680
Effective search space: 810708920
Effective search space used: 810708920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.8 bits)